The Effect of Probiotics Supplementation on the Gut Microbiome of Healthy Dogs Assessed Using Metagenomic Sequencing: A Randomized Control Trial

Abstract Objectives Dogs share similar gut microbiome (GM) with humans, making them a great model for investigating the effects of probiotics (PR) on GM and health. This randomized control trial examined changes in MB and health outcomes in household dogs after PR supplementation. Methods All dogs recruited were fed human grade cooked food ≥ 1 mo, not fed any cultured food, PR, prebiotics, or on antibiotics ≥ 3 mo, and absent of major diseases. Dogs were randomized to receive a daily dose of PR (20 billion CFU of L. reuteri, P. acidilactici, E. faecium, L. acidophilus, B. animalis, L. fermentum, L. rhamnosus) or placebo (PL) for 4 weeks. Owners completed a health survey and collected stool samples at baseline and 4 weeks after the intervention in both groups. Additional stool samples were collected 2 weeks after stopping the PR in the PR group. GM profiling was performed with metagenomic sequencing. Results Twenty three dogs in the PR and 19 dogs in the PL group completed the trial (5.6 ± 3.0 y, 69% male). PR had no effect on α-diversity. As compared to baseline, changes in β-diversity at the species level in 4.3% of GM were significantly affected by PR at week 4 (P < 0.001) but not at week 6. A significant increase (adj P < 0.01) for ≥ 2-fold in abundance was observed at week 4 as compared to baseline for 41 bacterial taxa, 29 (71%) of which belong in the Lactobacillus genus. The abundance of E. coli also decreased at week 4 in the PR group (2.8 folds, adj P < 0.01). The abundance of these taxa returned to baseline at week 6. Such changes in diversity or abundance were not observed with PL. Dogs fed PR tended to be at a lower risk of diarrhea during the trial (0% vs 16%, P = 0.08). No change in other health outcomes was observed. Conclusions Oral PR supplementation has a small but significant effect on GM in healthy dogs. Findings warrant further investigation with longer duration in populations at a higher risk of gastrointestinal diseases. Funding Sources NomNomNow Inc.

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The microbiota of healthy dogs demonstrates individualized responses to synbiotic supplementation in a randomized controlled trial

Animal Microbiome ◽

10.1186/s42523-021-00098-0 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Jirayu Tanprasertsuk ◽

Aashish R. Jha ◽

Justin Shmalberg ◽

Roshonda B. Jones ◽

LeeAnn M. Perry ◽

...

Keyword(s):

Gut Microbiota ◽

Bacterial Species ◽

Gastrointestinal Diseases ◽

Healthy Population ◽

Significant Shift ◽

Metagenomic Sequencing ◽

Β Diversity ◽

Shotgun Metagenomic Sequencing ◽

Populations At Risk ◽

Healthy Dogs

Abstract Background Probiotics have been demonstrated to ameliorate clinical signs of gastrointestinal diseases in dogs in various studies. However, the effect of probiotics in a healthy population, as well as factors contributing individualized responses, remain largely unknown. This trial examined gut microbiota (GM) and health outcomes in household dogs after synbiotic (SN) supplementation containing probiotics and inulin (a prebiotic). Healthy dogs were randomized to receive SN (50 mg/d inulin and 20 billion total CFU/d of L. reuteri, P. acidilactici, E. faecium, L. acidophilus, B. animalis, L. fermentum, L. rhamnosus) or placebo (PL) for 4 weeks. Owners completed a health survey and collected stool samples for GM profiling (shotgun metagenomic sequencing) at baseline and week 4 in both groups, and at week 6 in the SN group. Results A significant shift (p < 0.001) in β-diversity was observed in the SN (n = 24), but not PL group (n = 19), at week 4 relative to baseline. Forty-five bacterial species, 43 (96%) of which were Lactobacillales, showed an increase in the relative abundances (≥2 fold change, adjusted p < 0.05) in the SN group at week 4. E. coli also decreased at week 4 in the SN group (2.8-fold, adjusted p < 0.01). The altered taxa largely returned to baseline at week 6. The degree of changes in β-diversity was associated with GM at baseline. Specifically, dogs with higher Proteobacteria and lower Lactobacillales responded more robustly to supplementation in terms of the change in β-diversity. Dogs fed SN tended to have lower diarrhea incidence (0% vs 16%, p = 0.08). Conclusions SN supplement had a short-term impact on the gut microbiota in healthy household dogs as characterized by shotgun metagenomic sequencing. Findings warrant further investigation with longer duration and populations at risk of gastrointestinal diseases. The magnitude of response to the supplement was associated with microbial profile at baseline. To our knowledge, this is the first study documenting such association and may provide a basis for personalized nutrition in companion dogs.

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Gut microbiome of the emerald ash borer, Agrilus planipennis Fairmaire, and its relationship with insect population density

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa141 ◽

2020 ◽

Vol 96 (8) ◽

Author(s):

Judith Mogouong ◽

Philippe Constant ◽

Robert Lavallée ◽

Claude Guertin

Keyword(s):

Population Density ◽

Gut Microbiome ◽

Emerald Ash Borer ◽

Agrilus Planipennis ◽

Economic Damage ◽

Taxonomic Structure ◽

Rrna Gene ◽

Local Conditions ◽

Β Diversity ◽

Α Diversity

ABSTRACT The gut microbial communities of beetles play crucial roles in their adaptive capacities. Environmental factors such as temperature or nutrition naturally affect the insect microbiome, but a shift in local conditions like the population density on a host tree could also lead to changes in the microbiota. The emerald ash borer (EAB), Agrilus planipennis Fairmaire, is an exotic wood borer that causes environmental and economic damage to ash trees in North America. This study aimed to describe the taxonomic structure of the EAB gut microbiome and explore its potential relationship with borer population size. The number of EAB adults collected per tree through a 75 km transect from an epicenter allowed the creation of distinct classes of population density. The Gammaproteobacteria and Ascomycota predominated in bacterial and fungal communities respectively, as determined by sequencing of the bacterial 16S rRNA gene and the fungal internal transcribed spacer ITS2. Species richness and diversity of the bacterial community showed significant dependence on population density. Moreover, α-diversity and β-diversity analysis revealed some indicator amplicon sequence variants suggesting that the plasticity of the gut microbiome could be related to the EAB population density in host trees.

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Gut microbiome as a response marker for pancreatic enzyme replacement therapy in a porcine model of exocrine pancreas insufficiency

Microbial Cell Factories ◽

10.1186/s12934-020-01482-2 ◽

2020 ◽

Vol 19 (1) ◽

Author(s):

Sabrina Ritz ◽

Daniela Hahn ◽

Haleluya T. Wami ◽

Karin Tegelkamp ◽

Ulrich Dobrindt ◽

...

Keyword(s):

Enzyme Replacement Therapy ◽

Replacement Therapy ◽

Gut Microbiome ◽

Pancreatic Enzyme ◽

Microbial Composition ◽

Enzyme Replacement ◽

Β Diversity ◽

Healthy State ◽

Α Diversity ◽

Pancreatic Enzyme Replacement Therapy

Abstract Background Exocrine pancreatic insufficiency (EPI) is characterized by the loss of active pancreatic enzymes and a resulting severely reduced food digestion. EPI therapy requires orally applied pancreatic enzyme replacement. The gut microbiome is a known mediator of intestinal diseases and may influence the outcome of EPI and the effects of a pancreatic enzyme replacement therapy (PERT). Here, we analyzed the effects of EPI and PERT on the gut microbiome in the model of pancreatic duct ligated minipigs. Results The microbial community composition in pig feces was analyzed by next generation sequencing of 16S rRNA amplicons. The data were evaluated for α- and β-diversity changes and changes at the different Operational Taxonomic Unit (OTU) levels by Shannon–Wiener and inverse Simpson index calculation as well as by Principal Coordinates Analysis based on Bray–Curtis dissimilarity. Microbial α-diversity was reduced after EPI induction and reverted to nearly healthy state after PERT. Analysis of microbial composition and β-diversity showed distinctive clusters of the three study groups and a change towards a composition comparable to healthy animals upon PERT. The relative abundance of possible pathobionts like Escherichia/Shigella, Acinetobacter or Stenotrophomonas was reduced by PERT. Conclusion These data demonstrate that EPI-induced dysbiosis could be reverted by PERT to a nearly healthy state. Elevated α-diversity and the reduction of bacterial overgrowth after PERT promises benefits for EPI patients. Non-invasive microbiome studies may be useful for EPI therapy monitoring and as marker for response to PERT.

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Alterations in gut microbiome composition and function in irritable bowel syndrome and increased probiotic abundance with daily supplementation

10.1101/2021.09.02.458777 ◽

2021 ◽

Author(s):

Joann Phan ◽

Divya Nair ◽

Suneer Jain ◽

Thibaut Montagne ◽

Demi Valeria Flores ◽

...

Keyword(s):

Irritable Bowel Syndrome ◽

Gut Microbiome ◽

The United States ◽

Supporting Evidence ◽

Metagenomic Sequencing ◽

Healthy Controls ◽

Microbiome Composition ◽

Significant Difference ◽

Stool Samples ◽

Irritable Bowel

AbstractBackgroundIrritable bowel syndrome (IBS) is characterized by abdominal discomfort and irregular bowel movements and stool consistency. Because there are different symptoms associated with IBS, it is difficult to diagnose the role of the microbiome in IBS.ObjectiveHere, we present a study that includes metagenomic sequencing of stool samples from subjects with the predominant subtypes of IBS and a healthy cohort. We collected longitudinal samples from individuals with IBS who took daily made-to-order precision probiotic and prebiotic supplementation throughout the study.Materials and MethodsThis study includes a population of 489 individuals with IBS and 122 healthy controls. All stool samples were subjected to shotgun metagenomic sequencing. Precision probiotics and prebiotics were formulated for all subjects with longitudinal timepoints.ResultsThere was significant variation explained in the microbiome between the healthy and IBS cohorts. Individuals with IBS had a lower gut microbiome diversity and reduced anti-inflammatory microbes compared to the healthy controls. Eubacterium rectale and Faecalibacterium prausnitzii were associated with healthy microbiomes while Shigella species were associated with IBS. Pathway analysis indicated a functional imbalance of short chain fatty acids, vitamins, and a microbial component of Gram-negative bacteria in IBS compared to healthy controls. In the longitudinal dataset, there was a significant difference in microbiome composition between timepoints 1 and 3. There was also a significant increase in the overall microbiome score and relative abundances of probiotic species used to target the symptoms associated with IBS.ConclusionsWe identified microbes and pathways that differentiate healthy and IBS microbiomes. In response to precision probiotic supplementation, we identified a significant improvement in the overall microbiome score in individuals with IBS. These results suggest an important role for probiotics in managing IBS symptoms and modulation of the microbiome as a potential management strategy.ImportanceAn estimated 35 million people in the United States and 11.5% of the population globally are affected by IBS. Immunity, genetics, environment, diet, small intestinal bacterial overgrowth (SIBO), and the gut microbiome are all factors that contribute to the onset or triggers of IBS. With strong supporting evidence that the gut microbiome may influence symptoms associated with IBS, elucidating the important microbes that contribute to the symptoms and severity is important to make decisions for targeted treatment. As probiotics have become more common in treating IBS symptoms, identifying effective probiotics may help inform future studies and treatment.

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Fecal Microbiota Composition of a Mother-Infant Dyad in a Pig Model

Current Developments in Nutrition ◽

10.1093/cdn/nzaa054_087 ◽

2020 ◽

Vol 4 (Supplement_2) ◽

pp. 1015-1015

Author(s):

Julie Jeon ◽

Xi Fang ◽

Jeferson Lourenco ◽

Srujana Rayalam ◽

Michael Rothrock ◽

...

Keyword(s):

Gut Microbiome ◽

Maternal Nutrition ◽

Early Stage ◽

Illumina Miseq ◽

Well Being ◽

Fecal Microbiota ◽

Rrna Gene ◽

Gut Health ◽

Β Diversity ◽

Α Diversity

Abstract Objectives Microbial programming in early life is associated with gut health and overall well-being in adulthood. The establishment of the nascent gut microbiome is substantially influenced by both maternal nutrition and the native maternal microbiome. Pig is recognized as a valuable model in gastrointestinal track research due to its remarkable similarity to humans in gastrointestinal anatomy, physiology, biochemistry, immunology, and pathology. This study examined the characteristics of the gut microflora in the sow-piglet dyad. Methods Fecal samples were collected from sows (n = 6) and piglets (n = 24) at weaning. Bacterial DNA was isolated from the feces and the V3-V4 region of 16 s rRNA gene was amplified and sequenced using the Illumina Miseq platform and analyzed by QIIME pipeline. Results Sows had a twice higher abundance of Firmicutes than piglets (84.28% vs 40.19%, P < 0.0001), although Firmicutes was the most abundant phyla in both sows and piglets. Instead, piglets had higher abundances of Bacteroidetes (36.41% vs 9.61%, P < 0.0001) and Proteobacteria (11.31% vs 0.87%, P = 0.005) than sows. Early colonization of Proteobacteria has been suggested to be important for development of neonatal immunity. Firmicutes to Bacteroidetes ratio was higher in sows than in piglets (16.32 vs 1.36, P < 0.0001), which is consistent with previous reports in humans. The five most abundant families in sows were Clostridiaceae (30.43%), Turicibacteraceae (17.13%), Ruminococcaceae (11.29%), Lactobacillaceae (8.27%), and Lachnospiraceae (4.99%), while those in piglets were Bacteroidaceae (23.96%), Lachnospiraceae (9.13%), Clostridiaceae (7.52%), Ruminococcaceae (6.80%), and Enterobacteriaceae (6.63%). Observed OTUs in sows were higher (P = 0.02) than those in piglets, suggesting that piglets at early stage of life have lower fecal α-diversity. Moreover, β-diversity was very different between sows and piglets (P = 0.01). Conclusions Sows and piglets showed distinctive pattern of fecal microflora, and piglets had fewer species numbers at weaning compared to that of sows. This finding will provide a valuable information for future transgenerational studies on the gut microbiome and its consequences for health using a sow-piglet dyad. Funding Sources Georgia Experimental Agricultural Station, UGA Faculty research grant, and Center for Chronic Disorders of Aging at the PCOM.

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Cotrimoxazole Prophylaxis Increases Resistance Gene Prevalence and α-Diversity but Decreases β-Diversity in the Gut Microbiome of Human Immunodeficiency Virus–Exposed, Uninfected Infants

Clinical Infectious Diseases ◽

10.1093/cid/ciz1186 ◽

2019 ◽

Vol 71 (11) ◽

pp. 2858-2868 ◽

Cited By ~ 3

Author(s):

Alaric W D’Souza ◽

Eshia Moodley-Govender ◽

Bertram Berla ◽

Tejas Kelkar ◽

Bin Wang ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Antibiotic Resistance ◽

Resistance Gene ◽

Gut Microbiome ◽

Cotrimoxazole Prophylaxis ◽

Β Diversity ◽

Α Diversity ◽

Immunodeficiency Virus ◽

Functional Pathway ◽

Exposed Uninfected

Abstract Background Prophylactic cotrimoxazole treatment is recommended in human immunodeficiency virus (HIV)–exposed, uninfected (HEU) infants, but the effects of this treatment on developing HEU infant gut microbiotas and resistomes are largely undefined. Methods We analyzed whole-metagenome sequencing data from 163 longitudinally collected stool samples from 63 HEU infants randomized to receive (n = 34; CTX-T) or to not receive (n = 29; CTX-N) prophylactic cotrimoxazole treatment. We generated taxonomic, functional pathway, and resistance gene profiles for each sample and compared microbiome signatures between the CTX-T and CTX-N infants. Results Metagenomic analysis did not reveal significant differences in taxonomic or functional pathway α-diversity between CTX-T and CTX-N infants. In contrast, resistance gene prevalence (P = .00719) and α-diversity (P = .0045) increased in CTX-T infants. These differences increased over time for both resistance gene prevalence measured by log-normalized abundance (4-month mean, 0.71 [95% confidence interval {CI}, .2–1.2] and 6-month mean, 0.85 [95% CI, .1–1.7]) and α-diversity (P = .0045). Unlike α-diversity, interindividual gut microbiome taxonomic (mean, −0.11 [95% CI, −.15 to −.077]), functional taxonomic (mean, −0.050 [95% CI, −.084 to −.017]), and resistance gene (mean, −0.13 [95% CI, −.17 to −.099]) β-diversity decreased in CTX-T infants compared with CTX-N infants. These results are consistent with persistent antibiotic selection pressure. Conclusions Cotrimoxazole prophylaxis in HEU infants decreased gut microbiome β-diversity and increased antibiotic resistance gene α-diversity and prevalence. Antibiotic resistance is a growing threat, especially in low- and middle-income countries where the higher perinatal HIV exposure rates result in cotrimoxazole prophylaxis. Understanding effects from current HEU infant antibiotic prophylaxis guidelines will inform guideline revisions and efforts to reduce increasing antibiotic resistance.

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Metagenomic profiling of gut microbiome in early chronic kidney disease

Nephrology Dialysis Transplantation ◽

10.1093/ndt/gfaa122 ◽

2020 ◽

Author(s):

Noriaki Sato ◽

Masanori Kakuta ◽

Takanori Hasegawa ◽

Rui Yamaguchi ◽

Eiichiro Uchino ◽

...

Keyword(s):

Chronic Kidney Disease ◽

Kidney Disease ◽

Gut Microbiome ◽

Short Chain Fatty Acids ◽

Toxin Production ◽

Metagenomic Sequencing ◽

Stool Samples ◽

The Mean ◽

Estimated Glomerular Filtration Rates ◽

The Relationship

Abstract Background The relationship between chronic kidney disease (CKD) and the gut microbiome, which interact through chronic inflammation, uraemic toxin production and immune response regulation, has gained interest in the development of CKD therapies. However, reports using shotgun metagenomic analysis of the gut microbiome are scarce, especially for early CKD. Here we characterized gut microbiome differences between non-CKD participants and ones with early CKD using metagenomic sequencing. Methods In total, 74 non-CKD participants and 37 participants with early CKD were included based on propensity score matching, controlling for various factors including dietary intake. Stool samples were collected from participants and subjected to shotgun sequencing. Bacterial and pathway abundances were profiled at the species level with MetaPhlAn2 and HUMAnN2, respectively, and overall microbiome differences were determined using Bray–Curtis dissimilarities. Diabetic and non-diabetic populations were analysed separately. Results For diabetic and non-diabetic participants, the mean estimated glomerular filtration rates of the CKD group were 53.71 [standard deviation (SD) 3.87] and 53.72 (SD 4.44), whereas those of the non-CKD group were 72.63 (SD 7.72) and 76.10 (SD 9.84), respectively. Alpha and beta diversities were not significantly different between groups. Based on taxonomic analysis, butyrate-producing species Roseburia inulinivorans, Ruminococcus torques and Ruminococcus lactaris were more abundant in the non-CKD group, whereas Bacteroides caccae and Bacteroides coprocora were more abundant in the non-diabetic CKD group. Conclusions Although gut microbiome changes in individuals with early CKD were subtle, the results suggest that changes related to producing short-chain fatty acids can already be observed in early CKD.

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1771. Gut Resistome Changes in Response to Prophylactic Antibiotic Administration During Chemotherapy in Children With Acute Lymphoblastic Leukemia

Open Forum Infectious Diseases ◽

10.1093/ofid/ofy209.156 ◽

2018 ◽

Vol 5 (suppl_1) ◽

pp. S66-S66

Author(s):

Ellie Margolis ◽

Hana Hakim ◽

Jiangwei Yao ◽

Jason Rosch ◽

Li Tang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Acute Lymphoblastic Leukemia ◽

Community Composition ◽

Resistance Genes ◽

Gut Microbiome ◽

Lymphoblastic Leukemia ◽

Metagenomic Sequencing ◽

Pediatric Leukemia ◽

Drug Concentrations ◽

Stool Samples

Abstract Background Antibiotic resistance harbored in gut microbiome contributes to the emergence of multi–drug-resistant organisms (MDRO). Pediatric leukemia patients typically receive extensive antibiotics and are at higher risk for infection due to MDRO. Methods A prospective cohort of children (n = 242) with acute lymphoblastic leukemia self-collected stool samples at diagnosis and after induction chemothearpy. A third of patients (n = 69) underwent protocol-driven antibiotic prophylaxis: Levofloxacin (LV) given once neutropenia develops. With neutropenic fever patients on prophylaxis stopped LV and all patients received cefepime. Using metagenomic sequencing, we identified bacterial community composition and after alignment to the Comprehensive Antibiotic Resistance Database were able to determine the presence of bacterial resistance genes in 168 stool samples from 49 patients. Results Expected changes in the community composition were discovered with LV prophylaxis, including the loss of many Enterobacteriaceae and Enterococcaceae species, offset by increases in Bacteroides species. Unexpectedly, LV prophylaxis reduced the acquisition of VanA cluster of vancomycin resistance genes and did not increase acquisition of β-lactamase or fluoroquinolone (FQ) resistance gene families. Conclusion LV prophylaxis during leukemia treatment imparts predictable changes in gut bacterial communities but counter intuitively decreases antibiotic resistance in the gut microbiome reservoir. The reduction in VanA cluster of genes is likely due to depletion of Enterococcaceae species via direct killing or loss of synergistic partners. The lack of increase in target (FQ) or off-target resistance suggests that prophylaxis altered community selective pressures or prophylaxis drug concentrations were sufficient to limit the outgrowth of resistant mutants. Disclosures J. Wolf, Karius Inc.: Investigator, Research support.

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The Nursing Home Older Adult Gut Microbiome Composition Shows Time-dependent Dysbiosis and is Influenced by Medication Exposures, Age, Environment, and Frailty

The Journals of Gerontology Series A ◽

10.1093/gerona/glab167 ◽

2021 ◽

Author(s):

John P Haran ◽

Abigail Zeamer ◽

Doyle V Ward ◽

Protiva Dutta ◽

Vanni Bucci ◽

...

Keyword(s):

Older Adults ◽

Gut Microbiota ◽

Older Adult ◽

Gut Microbiome ◽

Assessment Tool ◽

Mini Nutritional Assessment ◽

Metagenomic Sequencing ◽

Mixed Effect ◽

Stool Samples ◽

Over Time

Abstract Older adults in nursing homes (NHs) have increased frailty, medication, and antimicrobial exposures, all factors that are known to affect the composition of gut microbiota. Our objective was to define which factors have the greatest association with the NH resident gut microbiota, explore patterns of dysbiosis and compositional changes in gut microbiota over time in this environment. We collected serial stool samples from NH residents. Residents were assessed using the Mini Nutritional Assessment tool and Clinical Frailty Scale. Bacterial composition of resident stool samples was determined by metagenomic sequencing. We used mixed-effect random forest modeling to identify clinical covariates that associate with microbiota. We enrolled and followed 166 residents from 5 NHs collecting 512 stool samples and following 15 residents for > 1 year. Medications, particularly psychoactive and anti-hypertensive medications, had the greatest effect on the microbiota. Age and frailty also contributed, and were associated with increased and decreased diversity, respectively. The microbiota of residents who had lived in the NH for > 1 year were enriched in inflammatory and pathogenic species and reduced in anti-inflammatory and symbiotic species. We observed intra-individual stability of the microbiome among older adults who had lived in the NH already for >1 year followed with sample collections 1 year apart. Older adult NH gut microbiome is heavily influenced by medications, age, and frailty. This microbiome is influenced by length of NH residence with dysbiosis becoming evident at 12 months, however after this point there is demonstrated relative stability over time.

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Vitamin D Metabolites and the Gut Microbiome in Older Men

Innovation in Aging ◽

10.1093/geroni/igaa057.3077 ◽

2020 ◽

Vol 4 (Supplement_1) ◽

pp. 840-840

Author(s):

Deborah Kado ◽

Robert Thomas ◽

Lingjing Jiang ◽

John Adams ◽

Rob Knight ◽

...

Keyword(s):

Vitamin D ◽

Gut Microbiome ◽

Forest Plot ◽

Vitamin D Metabolites ◽

Sequencing Data ◽

Operational Taxonomic Units ◽

Β Diversity ◽

Α Diversity ◽

Unweighted Unifrac ◽

Antidepressant Use

Abstract We examined the bidirectional impact of vitamin D on the composition and diversity of the gut microbiome in 567 MrOS men. Vitamin D metabolites were measured using LC-MSMS and stool sub-operational taxonomic units defined from 16S ribosomal RNA sequencing data using Deblur and Greengenes 13.8. Men’s mean serum level of 25(OH)D was in the sufficient range. Faith’s Phylogenetic Diversity and non-redundant covariate analyses revealed that 1,25(OH)2D explained 5% of variance in α-diversity; the other non-redundant covariates of site, race, recent antibiotic and antidepressant use explained another 6%. In β-diversity analyses using unweighted UniFrac, 1,25(OH)2D was the strongest factor assessed, explaining 2%. Random forest plot analyses identified 12 taxa, 6 in the phylum Firmicutes, positively associated with either 1,25(OH)2D and/or [1,25(OH)2D/25(OH)D] activation ratio. Higher levels of the active 1,25(OH)2D, but not 25(OH)D, were associated with butyrate producing bacteria. Men with favorable vitamin D activation profiles also had greater gut microbial diversity.

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